ISDA

Deposition Date 2008-12-19

Release Date 2009-04-28

Last Version Date 2023-12-13

Entry Detail

PDB ID:

2W6W

Keywords:

OXYGEN STORAGE

Title:

Crystal structure of recombinant Sperm Whale Myoglobin under 1atm of Xenon

Biological Source:

Source Organism:

PHYSETER CATODON (Taxon ID: 9755)

Host Organism:

ESCHERICHIA COLI

Method Details:

Experimental Method:

X-RAY DIFFRACTION

Resolution:

1.99 Å

R-Value Free:

0.20

R-Value Work:

0.18

R-Value Observed:

0.18

Space Group:

P 6

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Macromolecular Entities

Protein Blast

Polymer Type:polypeptide(L)
Molecule:MYOGLOBIN
Gene (Uniprot):MB
Chain IDs:A
Chain Length:154
Number of Molecules:1
Biological Source:PHYSETER CATODON

UniProt ID:P02185 Pfam ID:PF00042

Ligand Molecules

GOL

HEM

SO4

Primary Citation

Pattern of Cavities in Globins: The Case of Human Hemoglobin.

Savino, C, Miele, A.E, Draghi, F, Johnson, K.A, Sciara, G, Brunori, M, Vallone, B.Show

Biopolymers 91 1097 ? (2009)

PMID: 19365817 DOI: 10.1002/BIP.21201

Abstact

Our aim is to shed light on the conservation of potential ligand docking sites that play an important role in ligand dynamics of globins by using the technique of filling internal cavities naturally present in hemoglobin and myoglobin with xenon atoms. In particular, we present the high resolution structures of the Xe-adduct of deoxygenated wild type human hemoglobin and a quadruple mutant (L(B10)Y and H(E7)Q in alpha and beta chains). For the sake of comparison we also determined under the same experimental conditions the xenon complex of wild type sperm whale myoglobin. The analysis revealed that the number and position of Xe binding cavities are different in the alpha and beta subunits, the latter being more similar to myoglobin. Notably, no proximal Xe docking site was detected in hemoglobin, at variance with myoglobin. The pattern of internal cavities accessibility and affinity for xenon suggests a different role for the dynamics of ligand migration in the two types of hemoglobin chains as compared to myoglobin. The number and position of hydrophobic cavities in hemoglobin are briefly discussed also in comparison with the data available for other members of the globin superfamily.

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Primary Citation of related structures